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Plotting in R on the HPCΒΆ

When R is run on the HPC as a module, it will not be able to output plots due to the absence of a Graphical User Interface within the HPC. You might see errors such as: Unable to start device PNG or Unable to open connection to X11 display.

This can be solved by using an X Virtual Frame Buffer to run R in. The below is an example of how to do this:

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module load R/<version>
xvfb-run -a R

If, however, you do not want to write xvfb-run R each time, then you can set up an alias in your .bashrc file that will do this for you. Add the following line to your .bashrc file:

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alias R='xvfb-run -a R'

Within your R script there are a number of possible ways of saving plots. The following example uses base R:

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png("plot.png")
plot(1)
dev.off()

This will create a .png file called plot.png in the current working directory with your data plotted.

Alternatively, the tidyverse ggplot2 package can be used to save the plots to a variable which can be saved with the built-in ggsave() function. You should be able to save the generated plots bypassing the need to display them by using commands such as the following example within your RSCRIPT:

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library(ggplot2)
fig_1 <- ggplot(cars, aes(x = speed, y = dist)) + geom_point()
ggsave(fig_1, type = "cairo", file="fig_1.<extension>")

Note that tidyverse and base R can at times interfere with each other so we would recommend selecting one strategy for your plotting needs.

If you will always be loading the same version of R you will be able to create a bash function that will help you access the the functionality with a single command:

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function r_headless(){
module purge
module load lang/R/<version>
xvfb-run -a Rscript $1
}

The function can then be called on an R script as follows:

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r_headless script.R

We would recommend that you save the function to your .bashrc file so that the function is globally available.